recon-all T2 pial refinement fails

recon-all-output.txt

Step 0: recon-all -subjid H0351.1015 -all -i /data/allen/H0351.1015/T1.nii.gz -openmp 8 -notalairach

Step 1: recon-all -subjid H0351.1015 -T2 /data/allen/H0351.1015/T2.nii.gz -openmp 8

Step 2: recon-all -subjid H0351.1015 -T2pial -openmp 8

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /data/subjects
Actual FREESURFER_HOME /nitrc/usr/local/freesurfer
-rw-rw-r-- 1 root root 486104 Jul  5 13:42 /data/subjects/H0351.1015/scripts/recon-all.log
Linux master 3.2.0-39-virtual #62-Ubuntu SMP Thu Feb 28 00:48:27 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
#--------------------------------------------
#@# Refine Pial Surfs w/ T2/FLAIR Fri Jul  5 13:43:07 UTC 2013

 bbregister --s H0351.1015 --mov /data/subjects/H0351.1015/mri/orig/T2raw.mgz --lta /data/subjects/H0351.1015/mri/transforms/T2raw.lta --init-fsl --T2 

Log file is /data/subjects/H0351.1015/mri/transforms/T2raw.dat.log
Fri Jul  5 13:43:07 UTC 2013

setenv SUBJECTS_DIR /data/subjects
cd /data/subjects/H0351.1015/scripts
/nitrc/usr/local/freesurfer//bin/bbregister --s H0351.1015 --mov /data/subjects/H0351.1015/mri/orig/T2raw.mgz --lta /data/subjects/H0351.1015/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux master 3.2.0-39-virtual #62-Ubuntu SMP Thu Feb 28 00:48:27 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /nitrc/usr/local/freesurfer/
mri_convert /data/subjects/H0351.1015/mri/orig/T2raw.mgz /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/template.nii
mri_convert /data/subjects/H0351.1015/mri/orig/T2raw.mgz /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/template.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/subjects/H0351.1015/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, -1, 0)
writing to /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/template.nii...
fslregister --s H0351.1015 --mov /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/template.nii --reg /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/fslregister --dof 6 --fsvol brainmask.mgz
ERROR: you must have the FSLDIR environment variable defined and pointing to the FSL installation
mri_segreg --mov /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/template.nii --init-reg /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/reg.init.dat --out-reg /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/reg.init.dat
mri_segreg --mov /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/template.nii --init-reg /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/bbr.pass1.dat --out-reg /data/subjects/H0351.1015/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /data/subjects/H0351.1015/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /data/subjects/H0351.1015/mri/transforms/T2raw.dat.param --surf white --cur-reg /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open /data/subjects/H0351.1015/mri/transforms/tmp.bbregister.7105/bbr.pass1.dat
tkregister2_cmdl --mov /data/subjects/H0351.1015/mri/orig/T2raw.mgz --reg /data/subjects/H0351.1015/mri/transforms/T2raw.dat --noedit --ltaout /data/subjects/H0351.1015/mri/transforms/T2raw.lta
regio_read_register(): No such file or directory
Could not open /data/subjects/H0351.1015/mri/transforms/T2raw.dat
tkregister_tcl /nitrc/usr/local/freesurfer//tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /data/subjects/H0351.1015/mri/orig/T2raw.mgz
reg file       /data/subjects/H0351.1015/mri/transforms/T2raw.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
ERROR: reading /data/subjects/H0351.1015/mri/transforms/T2raw.dat
Cleaning up
 
Started at Fri Jul 5 13:43:07 UTC 2013 
Ended   at Fri Jul  5 13:43:08 UTC 2013
BBR-Run-Time-Sec 1
 
bbregister Done
To check results, run:
tkregister2 --mov /data/subjects/H0351.1015/mri/orig/T2raw.mgz --reg /data/subjects/H0351.1015/mri/transforms/T2raw.dat --surf
 

 mri_convert -at /data/subjects/H0351.1015/mri/transforms/T2raw.lta -rl /data/subjects/H0351.1015/mri/orig.mgz /data/subjects/H0351.1015/mri/orig/T2raw.mgz /data/subjects/H0351.1015/mri/T2.mgz 

mri_convert -at /data/subjects/H0351.1015/mri/transforms/T2raw.lta -rl /data/subjects/H0351.1015/mri/orig.mgz /data/subjects/H0351.1015/mri/orig/T2raw.mgz /data/subjects/H0351.1015/mri/T2.mgz 
ltaReadFile(/data/subjects/H0351.1015/mri/transforms/T2raw.lta): can't open file
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/subjects/H0351.1015/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, -1, 0)
INFO: Reading transformation from file /data/subjects/H0351.1015/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
No such file or directory
ERROR: Reading transform from file /data/subjects/H0351.1015/mri/transforms/T2raw.lta
Linux master 3.2.0-39-virtual #62-Ubuntu SMP Thu Feb 28 00:48:27 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s H0351.1015 exited with ERRORS at Fri Jul  5 13:43:09 UTC 2013

For more details, see the log file /data/subjects/H0351.1015/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting